Description Usage Arguments Value See Also Examples
View source: R/rd.cnSegments.R
uses Circular Binary Segmentation (as implemented in the DNAcopy package) to segment the genome and returns regions that contain CN gains or losses
1 | rd.cnSegments(rdo, onlyAlts=FALSE, minWidth=2, alpha=0.01, rmGaps=TRUE)
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rdo |
a readDepth object created with new("rdObject") and filled with read counts using the readDepth() command |
onlyAlts |
whether the function should return just those segments that exceed the threshold values for gain and loss The Default is FALSE, which returns all segments. |
minWidth |
the minimum number of consecutive aberrant bins required before making a segment call. Default is two |
alpha |
the significance level for the CBS to accept change-points. Default 0.01 |
rmGaps |
Controls whether adjacent segments have their boundaries adjusted to remove gaps. If so, the new segment boundary is set to halfway between the existing boundary calls. |
returns a dataframe with 5 columns: chr start stop #probes copynumber
'readDepth'
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | #create a rdObject, set bin params
# x <- new("rdObject")
#fill the bins with reads
# x.reads <- readDepth(x)
#do mapability correction on the read counts
# x.map <- rd.mapCorrect(x.reads)
#do gc correction on the read counts
# x.gcCorr <- rd.gcCorrect(x.map)
#return regions of CN gain and loss
# segs <- rd.cnSegments(x.gcCorr)
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